TF reporter barcode processing - Deep P53/GR scan - stimulation 2

Introduction

12,000 TF reporters on pMT06 were transfected into A549 & MCF7 cells, sequencing data yielded barcode counts of these experiments. These counts will be processed in this script.

Analysis

Data exploration

Stuff learned from above figures:
-> Based on these figures I will exclude all samples that have less than 300 barcodes with at least 500 normalized counts.

Session Info

paste("Run time: ",format(Sys.time()-StartTime))

## [1] "Run time:  2.717482 mins"

getwd()

## [1] "/DATA/usr/m.trauernicht/projects/SuRE_deep_scan_trp53_gr/stimulation_2_gcf6301"

date()

## [1] "Tue Jan 12 11:10:28 2021"

sessionInfo()

## R version 3.6.3 (2020-02-29)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 16.04.7 LTS
## 
## Matrix products: default
## BLAS:   /usr/lib/libblas/libblas.so.3.6.0
## LAPACK: /usr/lib/lapack/liblapack.so.3.6.0
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
##  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
##  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
## 
## attached base packages:
## [1] grid      parallel  stats     graphics  grDevices utils     datasets 
## [8] methods   base     
## 
## other attached packages:
##  [1] viridis_0.5.1        viridisLite_0.3.0    ggpointdensity_0.1.0
##  [4] ggbiplot_0.55        scales_1.1.0         factoextra_1.0.7    
##  [7] shiny_1.4.0          pheatmap_1.0.12      gridExtra_2.3       
## [10] RColorBrewer_1.1-2   readr_1.3.1          haven_2.2.0         
## [13] ggbeeswarm_0.6.0     plotly_4.9.2.1       tibble_3.0.1        
## [16] dplyr_0.8.5          vwr_0.3.0            latticeExtra_0.6-29 
## [19] lattice_0.20-38      stringdist_0.9.5.5   GGally_1.5.0        
## [22] ggpubr_0.2.5         magrittr_1.5         ggplot2_3.3.0       
## [25] stringr_1.4.0        plyr_1.8.6           data.table_1.12.8   
## 
## loaded via a namespace (and not attached):
##  [1] httr_1.4.1        tidyr_1.0.0       splines_3.6.3     jsonlite_1.7.1   
##  [5] prettydoc_0.4.0   assertthat_0.2.1  vipor_0.4.5       yaml_2.2.1       
##  [9] ggrepel_0.8.1     pillar_1.4.3      glue_1.4.2        digest_0.6.27    
## [13] promises_1.1.1    ggsignif_0.6.0    colorspace_1.4-1  Matrix_1.2-18    
## [17] htmltools_0.5.0   httpuv_1.5.4      pkgconfig_2.0.3   purrr_0.3.3      
## [21] xtable_1.8-4      jpeg_0.1-8.1      later_1.1.0.1     mgcv_1.8-31      
## [25] farver_2.0.1      ellipsis_0.3.0    withr_2.1.2       lazyeval_0.2.2   
## [29] crayon_1.3.4      mime_0.9          evaluate_0.14     nlme_3.1-143     
## [33] forcats_0.4.0     beeswarm_0.2.3    tools_3.6.3       hms_0.5.3        
## [37] lifecycle_0.2.0   munsell_0.5.0     compiler_3.6.3    rlang_0.4.8      
## [41] htmlwidgets_1.5.2 crosstalk_1.0.0   labeling_0.3      rmarkdown_2.5    
## [45] gtable_0.3.0      reshape_0.8.8     reshape2_1.4.4    R6_2.5.0         
## [49] knitr_1.30        fastmap_1.0.1     stringi_1.5.3     Rcpp_1.0.5       
## [53] vctrs_0.2.4       png_0.1-7         tidyselect_1.1.0  xfun_0.19